I don't see why there is any argument over top/bottom vs. sides...maybe it's because I run hotter disks than everybody else.
As BladeRunner said, the heat generated from drives is not much, and is more of a 'heat soak' built up over time. Even though, it is still obvious that the sides are the ideal place to cool the drive.
1. Look at high-end, high-heat SCSI disks--they have fins BUILT INTO the aluminum chassis. Examples: the six-platter(!) IBM 36Z15s that I run. Or the Fujitsu MAM/MAN/MAP/MAS, Maxtor/Quantum Atlas XX, WD Raptor (SATA=SCSI lite), etc.
2. Also note that drive lids are made of STEEL, and sometimes is several layers thick, withouth TIMs. Not to mention, drive lids tend to be very smooth, with obviously no attempt made to increase surface area via fins or ripples.
3. What about the massive insulating PLASTIC STICKERS that are on top of the drives?
Obviously the engineers had no intentions to dissipate significant amounts of heat through the lid--they expected it to leave through the main aluminum chassis, which contacts both the spindle motor AND the heated gas inside the drive.
If heat was to be discharged through the lid, it would be aluminum, and the labels would be smaller or nonexistent, i.e. etched into the lid (or stencilled on like Quantum used to do). Also, there would be at least some attempt made to stamp little fins in to increase the surface area.
As far as the controller board goes, there is little sense in cooling it. They are almost always insulated from the main body of the drive by a nonconductive plastic sheet, and a think sheet of foam, except where a few screws attach them to the drive, and where control electrodes pass into the body. In the worst case, very few components on the board will generate enough heat to put themselves at a high temp. Most of those are spec'd to run at even higher temps. Of those that remain (probably none), they can be cooled with a tiny passive heatsink.
Kindly disregard:
1. Plexi cases. They are a very recent development, and are almost certainly NOT considered when drives are engineered. (especially SCSI drives, which usually end up in servers)
2. Drive rails. More common, but are most commonly used with high CFM fans in a server for hot-swap applications, so the entire drive gets airflow, and heat dissipation through the rails is not a concern. If you are thinking of the plastic rails in 5.25" bays, please remember that those are intended for optical/tape/front expansion, not hard drives. Also, nearly all 3.5"->5.25" bay-conversion kits for HDDs include a fan.